Graphviz not running in jupyter notebook python = 3.6?

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06-10-2024

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Graphviz Not Working in Jupyter Notebook with Python 3.6? Here's the Fix!

Tired of Graphviz refusing to render your beautiful graphs within your Jupyter Notebook, especially with Python 3.6? You're not alone! This frustrating issue often pops up due to compatibility conflicts between the Graphviz library and the Python version.

Here's a simplified breakdown of the problem:

• Graphviz is a powerful tool for visualizing graphs.
• Jupyter Notebook is a popular environment for interactive coding.
• Python 3.6 has certain limitations that can clash with Graphviz's requirements.

Let's dive into a real-world scenario:

import graphviz
dot = graphviz.Digraph(comment='The Round Table')
dot.node('A', 'King Arthur')
dot.node('B', 'Sir Lancelot')
dot.node('C', 'Sir Galahad')
dot.edges(['AB', 'AC'])
dot.render('round-table.gv', view=True)

Expected Output: A beautifully rendered graph of the "Round Table" displayed in your Jupyter Notebook.

Actual Output: An error message, often related to Graphviz's inability to find the necessary libraries or execute the rendering process.

Troubleshooting the Issue:

The root cause of the problem lies in compatibility issues between Graphviz and specific Python versions. Python 3.6 may lack the necessary dependencies for Graphviz to function correctly. Here's what you can do:

1. Check Your Graphviz Installation:

• Verify Graphviz is Installed: Open your terminal (or command prompt) and run:

  dot -V
  

  If Graphviz is correctly installed, you should see its version information.

• Install Graphviz (if not already installed):

  • Linux:

    sudo apt-get install graphviz
    

  • macOS:

    brew install graphviz
    

  • Windows: Download and install from the official website: https://graphviz.org/download/

2. Update Your Python and Jupyter Notebook:

While Python 3.6 is no longer the latest version, if you're unable to upgrade, consider these options:

• Update Jupyter Notebook:

  pip install --upgrade jupyter
  

• Use a Virtual Environment:
  Creating a virtual environment ensures you're using specific libraries and versions for each project, minimizing conflicts.

  python3 -m venv myenv
  source myenv/bin/activate 
  

  Then, install Graphviz and Jupyter Notebook within this environment.

3. Use an Alternative Library (for Python 3.6):

If the above solutions don't work, you can try alternatives to the graphviz library:

• Pydot:

  pip install pydot
  

  • You can use it with graphviz to generate the graph:

  from pydot import Dot, Node, Edge
  graph = Dot(graph_type='digraph', comment='The Round Table')
  graph.add_node(Node('A', label='King Arthur'))
  graph.add_node(Node('B', label='Sir Lancelot'))
  graph.add_node(Node('C', label='Sir Galahad'))
  graph.add_edge(Edge('A', 'B'))
  graph.add_edge(Edge('A', 'C'))
  graph.write_png('round-table.png')
  

Additional Tips:

• Restart Your Notebook Kernel: Restarting the Jupyter Notebook kernel often resolves minor glitches.
• Check for Missing Dependencies: Ensure all necessary Python packages are installed.

Conclusion:

By addressing the compatibility issues between Graphviz and Python 3.6, you can finally visualize your graphs within your Jupyter Notebook. Remember to always check your installation and explore alternatives if needed. Good luck!